| --- |
| language: |
| - en |
| pretty_name: CTD Pretrain Corpus (v1, capped) |
| tags: |
| - pretraining |
| - clinical-trials |
| - fda |
| - pmc |
| - sql |
| - python |
| - text-generation |
| configs: |
| - config_name: clinical_trials |
| data_files: clinical_trials.jsonl |
| - config_name: generic |
| data_files: generic.jsonl |
| - config_name: python |
| data_files: python.jsonl |
| - config_name: sql |
| data_files: sql.jsonl |
| - config_name: fda |
| data_files: fda.jsonl |
| - config_name: pmc |
| data_files: pmc.jsonl |
| - config_name: generators_t0_llm |
| data_files: t0_llm.jsonl |
| - config_name: generators_t1 |
| data_files: t1.jsonl |
| - config_name: generators_t2_dedup |
| data_files: t2_dedup.jsonl |
| - config_name: generators_t3_q_dedup |
| data_files: t3_q_dedup.jsonl |
| - config_name: generators_t4_kpis_v2_relations |
| data_files: t4_kpis_v2_relations.jsonl |
| - config_name: generators_t5_templated |
| data_files: t5_templated.jsonl |
| - config_name: generators_t7 |
| data_files: t7.jsonl |
| --- |
| |
| # CTD Pretrain Corpus — v1 (capped) |
|
|
| Pretraining corpus assembled from clinical-trial, regulatory, biomedical-literature, |
| code, SQL, and synthetic-generator sources. Every record is a JSON object with a |
| `text` field (plus source-specific `metadata`/`source` fields). |
|
|
| This is the **v1 / capped** release: each source category was streamed in file |
| order and truncated once its configured token budget was reached (whole-record |
| cutoff — the record that crosses the limit is kept, so totals land at or just |
| over the stated cap). Categories with no configured limit (`generators`) are |
| included in full. The uncapped/full version of every category lives in the |
| sibling `processed-all` release. |
|
|
| Token counts were computed with the local tokenizer at |
| `overall/v1/qwen3.5-0.8b` (Qwen 3.5 0.8B tokenizer), counting the `text` field |
| only, with `add_special_tokens=False`. |
|
|
| ## Overall stats |
|
|
| | Category | Tokens | Records | Token limit | Limit reached | Files | |
| |---|---|---|---|---|---| |
| | clinical_trials | 1,000,000,017 | 222,238 | 1,000,000,000 | yes | `clinical_trials.jsonl` | |
| | generators | 892,358,213 | 705,472 | — (no limit) | no | `t0_llm.jsonl`, `t1.jsonl`, `t2_dedup.jsonl`, `t3_q_dedup.jsonl`, `t4_kpis_v2_relations.jsonl`, `t5_templated.jsonl`, `t7.jsonl` | |
| | generic | 500,000,092 | 725,848 | 500,000,000 | yes | `generic.jsonl` | |
| | python | 400,000,261 | 486,395 | 400,000,000 | yes | `python.jsonl` | |
| | sql | 400,009,402 | 54,065 | 400,000,000 | yes | `sql.jsonl` | |
| | fda | 150,000,137 | 1,694,490 | 150,000,000 | yes | `fda.jsonl` | |
| | pmc | 300,022,934 | 29,776 | 300,000,000 | yes | `pmc.jsonl` | |
| | **Total** | **3,642,391,056** | **3,918,284** | | | | |
|
|
| ## Generators — per-file breakdown |
|
|
| The `generators` category has no token cap, so every source file is included |
| in full. Individual file stats: |
|
|
| | File | Records | Tokens | |
| |---|---|---| |
| | `t0_llm.jsonl` | 12,473 | 13,544,109 | |
| | `t1.jsonl` | 637,765 | 765,998,078 | |
| | `t2_dedup.jsonl` | 30,998 | 6,123,972 | |
| | `t3_q_dedup.jsonl` | 9,839 | 92,449,908 | |
| | `t4_kpis_v2_relations.jsonl` | 92 | 1,542,592 | |
| | `t5_templated.jsonl` | 14,184 | 12,266,811 | |
| | `t7.jsonl` | 121 | 432,743 | |
| | **Subtotal (generators)** | **705,472** | **892,358,213** | |
|
|
| ## Source categories |
|
|
| - **clinical_trials** — clinical trial records (from `ct-v1/ct-v1.jsonl`), single merged file. |
| - **generators** — synthetic/templated data-generation outputs (`t0`–`t7` pipeline stages), kept as individual files, no cap applied. |
| - **generic** — general-domain text sampled from a ~750M-token pool (`generic/all-750M/*.parquet`), merged into one file. |
| - **python** — Python/code + visualization datasets (`python/*.parquet`), merged into one file. |
| - **sql** — SQL Q&A / schema data (`sql/*.arrow`), merged into one file. |
| - **fda** — FDA regulatory pretraining text (`fda_pretrain_full.jsonl`). |
| - **pmc** — PubMed Central biomedical literature (`pmc.jsonl`). |
| |
| ## Format |
| |
| Each file is newline-delimited JSON (`.jsonl`). Every record contains at least: |
| |
| ```json |
| {"text": "...", "metadata": {...}} |
| ``` |
| |
| `metadata`/`source` fields vary by category and reflect the original upstream schema. |
| |
| ## Tokenizer |
| |
| - Path: `overall/v1/qwen3.5-0.8b` |
| - Counting method: `Tokenizer.encode_batch(texts, add_special_tokens=False)`, token count = `len(encoding.ids)` per record's `text` field. |
| |
| ## Files in this release |
| |
| See `stats.json` / `stats.md` in this directory for the machine-readable and |
| tabular versions of the stats above. |
| |
